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CHANGED: bumped to py3.13 #87

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Merged
josenimo merged 5 commits into from
Oct 18, 2025
Merged

CHANGED: bumped to py3.13 #87

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391e711
CHANGED: gensim ~=4.4, scipy ~=1.13
josenimo Oct 18, 2025
45dd773
ADDED: python 3.13 to testing matrix
josenimo Oct 18, 2025
05d945b
ADDED: spatialdata 0.5 optional
josenimo Oct 18, 2025
e262d19
Loosened xarray dependencies
josenimo Oct 18, 2025
8278238
numpy >2
josenimo Oct 18, 2025
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2 changes: 1 addition & 1 deletion .github/workflows/test.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ jobs:
fail-fast: false
matrix:
os: [windows-latest, macos-latest, ubuntu-latest ]
python: ["3.11", "3.12"]
python: ["3.11", "3.12", "3.13"]

env:
OS: ${{ matrix.os }}
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21 changes: 11 additions & 10 deletions pyproject.toml
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@@ -1,34 +1,35 @@
[project]
name = "openDVP"
version = "0.7.2"
version = "0.7.3"
description = "open-sourced Deep Visual Proteomics toolkit"
readme = "README.md"
requires-python = ">=3.11, <3.13"
requires-python = ">=3.11, <3.14"
license = {file = "LICENSE"}
authors = [{name = "Jose Nimo", email = "jose.nimo@mdc-berlin.de"}]
maintainers = [{ name = "Jose Nimo", email = "jose.nimo@mdc-berlin.de" }]

dependencies = [
"spatialdata == 0.4.0",
"numpy >= 2.0.0",
"spatialdata >= 0.4.0",
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Copilot AI Oct 18, 2025

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The dependency constraint for spatialdata was changed from exact version (==) to minimum version (>=), which may introduce breaking changes. Since the previous version was pinned to 0.4.0, consider using a pessimistic constraint like ~= 0.4.0 to allow patch updates while preventing breaking minor version changes.

Suggested change
"spatialdata >= 0.4.0",
"spatialdata ~= 0.4.0",

Copilot uses AI. Check for mistakes.
"napari-spatialdata == 0.5.5",
"spatialdata-plot ~= 0.2.9 ",
"ipykernel ~= 6.25",
"scanpy >=1.11, <1.14",
"loguru ~= 0.7.3",
"scipy <1.13", # Gensim breaks above
"scipy ~= 1.13",
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Copilot AI Oct 18, 2025

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The constraint changed from <1.13 to ~= 1.13, which now requires scipy version 1.13 or higher (but <2.0). The comment 'Gensim breaks above' was removed, but this constraint may still cause issues if gensim is incompatible with scipy 1.13+. Verify that gensim 4.4.0 is compatible with scipy 1.13+.

Suggested change
"scipy ~= 1.13",
"scipy <1.13", # Gensim breaks above 1.13

Copilot uses AI. Check for mistakes.
"statsmodels >=0.14.5",
"adjusttext",
"pingouin >=0.5.5, <0.6",
"esda >=2.7, <2.8",
"upsetplot",
"perseuspy >=0.3.9,<0.4",
"gensim >=4.3.2", # Gensim breaks with python >=3.13
"gensim ~=4.4.0",
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Copilot AI Oct 18, 2025

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The gensim version was updated from >=4.3.2 to ~=4.4.0, and the comment 'Gensim breaks with python >=3.13' was removed. Verify that gensim 4.4.0 actually supports Python 3.13, as the comment removal suggests this was a blocker for Python 3.13 support.

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"pyqt6",
"tifffile ~= 2025.9.30",
"scikit-image ~= 0.25.2",
"scikit-learn ~= 1.7.2",
"xarray ~= 2024.11.0",
"pyogrio ~= 0.11.1"
"tifffile >= 2025.9.30",
"scikit-image >= 0.25.2",
"scikit-learn >= 1.7.2",
"xarray >= 2024.11.0",
"pyogrio >= 0.11.1"
]

[dependency-groups]
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